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E-raamat: Applying Genomic and Proteomic Microarray Technology in Drug Discovery

(QuantiScientifics, LLC, Irvine, California, USA)
  • Formaat: 322 pages
  • Ilmumisaeg: 13-Mar-2013
  • Kirjastus: CRC Press Inc
  • Keel: eng
  • ISBN-13: 9781439855645
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  • Formaat: 322 pages
  • Ilmumisaeg: 13-Mar-2013
  • Kirjastus: CRC Press Inc
  • Keel: eng
  • ISBN-13: 9781439855645
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Microarrays play an increasingly significant role in drug discovery. The commercial landscape has changed dramatically over the past few years and researchers have made great advancements with regard to construction and use. Now in its second edition, Applying Genomic and Proteomic Microarray Technology in Drug Discovery highlights, describes, and evaluates current scientific research using microarray technology in genomic and proteomic applications.

Updated and revised to reflect recent progress in the field, the second edition discusses:

  • Expanded omics-driven applications, including the areas of metabolomics and chemical biology
  • The commercialization of the microarray platform, with a historical perspective aimed at recognizing key technological developments
  • Solid-supports (substrates) and surface chemistries currently used in the creation of nucleic acid and protein microarrays
  • Different approaches to producing microarrays that achieve spot equality with the same number of molecules properly oriented
  • The development of the gene expression microarray and representative applications
  • The development of protein microarray technology, including its history and key applications

Unique to this edition is a new chapter on multiplex assays that examines the development and applications of arrays across diverse platforms. It discusses applications for qPCR, multiplex lateral flow, and multiplex bead assays. It also presents platform-to-platform comparisons.

Microarrays remain an invaluable tool for omics-based research not only in drug discovery, but in the life sciences, in clinical research, and for diagnostic applications worldwide. This volume presents the current state of the art on the utility of this technology to solve a host of important biological problems.

Arvustused

"This publication offers a detailed perspective and insight into the present and future uses of this technology" Anticancer Research

"A basic reference on the benefits of microarray technology in drug discovery, this publication offers a detailed perspective and insight into the present and future uses of this technology." Anticancer Research

Preface xiii
The Author xv
Chapter 1 Omics and Microarrays Revisited
1(30)
Introduction
1(2)
The Microarray Format
3(1)
Terms and Definitions
3(3)
General Utility
6(1)
The Biomedical Testing Continuum
6(1)
Biotech Sector Trends Revisited
7(1)
The Omic Era
8(4)
The Role for Gene Expression Microarrays in Drug Discovery
12(3)
Toxicogenomic Applications
15(1)
Proteomics Today-The Great Challenge
16(1)
The Potential Role for Protein Microarrays in Drug Discovery
17(1)
Critical Issues with Protein Microarrays
18(1)
Stability and Performance
18(2)
Content
20(1)
Detection
20(1)
Micro-ELISA Formats
21(1)
Protein Profiling Formats
22(1)
Near-Term Biomedical Applications
22(1)
Cytokines
22(1)
Autoimmune Diseases and Allergy
23(1)
Future Medicine-Pharmacoproteomics or Pharmacogenomics?
24(3)
References
27(4)
Chapter 2 Commercial Microarrays
31(26)
Introduction
31(1)
In Situ DNA Arrays
31(8)
Ex Situ or Spotted DNA Arrays
39(1)
Content for DNA Microarrays
40(1)
Suppliers of DNA Microarrays
41(1)
Comparison of Commercial DNA Microarrays
41(3)
Commercial Protein Arrays
44(1)
Content Providers
45(1)
An Open Platform Approach
46(1)
A2 Multiplex ELISA System
46(2)
Three-Dimensional (3D) and Four-Dimensional (4D) Chips
48(1)
Flow-Thru Biochips
49(2)
Electronic Biochips
51(3)
References
54(3)
Chapter 3 Supports and Surface Chemistries
57(46)
Introduction
57(1)
Substrates
57(1)
Membrane Substrates
58(3)
Glass Substrates
61(1)
Covalent Attachment
61(3)
Adsorptive Attachment
64(4)
Plastic Substrates
68(3)
Physical Features
71(1)
Hydrogels
71(1)
Surface Chemistries
72(1)
Linkers
72(9)
Reactive Groups
81(4)
Preparation of Glass Substrates for Derivatization
85(3)
Variation in the Performance of Glass Slide-Based Antibody Microarrays
88(2)
Comparison of Different Surface Chemistries for the Immobilization of Auto-Antigens
90(1)
Click Chemistry as an Immobilization Strategy
91(2)
Oxygen Plasma-Mediated Modification of DVD-R Disks for Tethering of Oligonucleotides
93(3)
Construction of Lipid Bilayer Microarrays
96(1)
Summary
97(1)
References
98(5)
Chapter 4 Arraying Processes
103(66)
Introduction
103(1)
Creating Spotted Microarrays
104(1)
Substrates
104(1)
Print Buffer
105(1)
The Printing Environment
106(1)
Microarray Printing Mechanisms
106(7)
Microarray Pins
113(2)
Other Approaches
115(6)
Printer Performance
121(1)
Pin Performance
121(4)
Microarray Design
125(3)
Setting Up the Print Run
128(2)
Printing Parameters
130(3)
Preparing the Probe Ink
133(1)
Optimization of Probe Concentration
133(1)
Protocols for Printing Nucleic Acids
134(1)
cDNA Microarray
134(1)
Oligonucleotides
135(1)
Use of DMSO
136(1)
Use of Betaine
136(2)
Use of Polyvinyl Alcohol
138(1)
Evaporation
138(3)
Print Quality Assessment
141(3)
Backgrounds
144(2)
Protocols for Printing Proteins
146(2)
Antibody Arrays
148(5)
Newer Methods for Printing
153(1)
Acoustic Dispensing
153(2)
Flexographic Printing
155(2)
Microarray-to-Microarray Slide Snapping Transfer
157(1)
Micro-Contact (CP) Printing
158(3)
Creation of Peptide Nucleic Acid Microarrays by CP
161(2)
Covalent Subtractive Print by CP
163(1)
References
164(5)
Chapter 5 Gene Expression: Microarray-Based Applications
169(48)
Introduction
169(1)
Applications Demonstrating DNA Microarray Utility
169(1)
Gene Expression
169(11)
Biomedical Research Applications
180(1)
Drug Discovery
180(2)
Drug Toxicity
182(3)
Cancer
185(12)
Infectious Disease
197(3)
Other Disease States
200(3)
Micro-RNA
203(1)
The Utility of Gene Expression Microarrays in Micro-RNA Analysis
204(2)
The Nature of Platform-to-Platform Disparity
206(4)
Array-Based Comparative Genomic Hybridization
210(1)
Karyotype, Fluorescence in situ Hybridization (FISH), Comparative Genomic Hybridization (CGH), or Array-CGH?
211(2)
References
213(4)
Chapter 6 Protein Microarray Applications
217(50)
Introduction
217(1)
Spot Theory
217(6)
Applications Demonstrating Protein Microarray Utility
223(1)
Microtiter-Based Antibody Arrays
224(1)
Membranes
225(3)
Glass Slides
228(7)
Measuring Microarray Performance
235(1)
Sensitivity and Dynamic Range
235(7)
Other Microarray Formats Useful for Proteomic Applications
242(1)
mRNA-Protein Fusions
242(2)
PISA
244(2)
Aptamers
246(3)
Universal Protein Array
249(5)
Peptide Arrays for Antibody Detection
254(1)
Phage-Display Antibody Selection
255(1)
Protein Kinase Microarray
255(1)
Protein Microarrays Useful in Auto-Antibody Screening
256(2)
Dual Labeling of Targets for Increased Sensitivity and Specificity
258(1)
The Depletion of Highly Abundant Proteins from Serum Deemed Unnecessary
259(1)
Competitive ELISA by Protein Microarray
259(1)
The Issue of Cross-Reactivity in a Protein Microarray Sandwich ELISA
260(3)
References
263(4)
Chapter 7 Multiplex Assays
267(28)
Introduction
267(1)
Benefit
267(1)
Definition
267(4)
Multiplex Polymerase Chain Reaction (PCR)
271(1)
Multiplex PCR Compared to DNA Microarray
272(1)
Multiplex Lateral Flow
272(2)
Nucleic Acid Lateral Flow Immunoassay (NALFIA)
274(2)
Multiple Test Lines
276(1)
Multiplex Bead-Based Assays
276(1)
Multiplex Bead-Based Assay Compared to the ELISA
277(2)
Multiplex Bead-Based Herpes Simplex Virus (HSV) Assay Compares Favorably with Serological Methods
279(2)
False Readings
281(1)
Observed Differences between ELISA and Bead-Based Multiplex
281(1)
Combined Multiplex PCR and Multiplex Bead-Based Assay
282(1)
Multiplex Microarrays
283(1)
Multiplex Microarray Plate Assay Compared to the ELISA
284(2)
A Lack of Standardization
286(1)
Label Free Detection of a Multiplex Small Molecule Microarray
286(2)
Adoption of Multiplex Assays
288(2)
Trends
290(1)
References
291(4)
Index 295
Robert S. Matson is president and co-founder of QuantiScientifics, LLC. The company is involved in the commercialization of multiplexed assays for life science, clinical research, and in vitro diagnostics. Previously, Matson was involved in the research and development of microarray technologies, detection chemistries, as well as point-of-care devices for more than 17 years while at Beckman Coulter, Inc. He participated in the National Institute of Standards and Technologys (NIST) Advanced Technology Program sponsored Genosensor Consortium and collaborated with Sir Edwin Southern on the development of an in situ oligonucleotide array synthesis platform for the corporation. Other work included development of the A2 MicroArray System, a microplate-based array platform for multiplexed micro-ELISA, which QuantiScientifics recently licensed for commercialization.